4HHJ

Dengue serotype 3 RNA-dependent RNA polymerase

PDB DOI: https://doi.org/10.2210/pdb4HHJ/pdb

Classification: TRANSFERASE
Organism(s): dengue virus type 3
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-10-10 Released: 2013-02-27
Deposition Author(s): Noble, C.G., Lescar, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 ?
R-Value Free: 0.209
R-Value Work: 0.177
R-Value Observed: 0.178

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Conformational flexibility of the Dengue virus RNA-dependent RNA polymerase revealed by a complex with an inhibitor

Noble, C.G., Lim, S.P., Chen, Y.L., Liew, C.W., Yap, L., Lescar, J., Shi, P.-Y.

(2013) J Virol 87: 5291-5295

PubMed: 23408636 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1128/JVI.00045-13
Primary Citation of Related Structures:
3VWS, 4HHJ

PubMed Abstract:
We report a highly reproducible method to crystallize the RNA-dependent RNA polymerase (RdRp) domain of dengue virus serotype 3 (DENV-3), allowing structure refinement to a 1.79-? resolution and revealing amino acids not seen previously. We also present a DENV-3 polymerase/inhibitor cocrystal structure at a 2.1-? resolution. The inhibitor binds to the RdRp as a dimer and causes conformational changes in the protein. The improved crystallization conditions and new structural information should accelerate structure-based drug discovery.

Organizational Affiliation

Novartis Institute for Tropical Diseases, Singapore, Singapore.

Macromolecule Content

Total Structure Weight: 74.36 kDa
Atom Count: 5,524
Modelled Residue Count: 588
Deposited Residue Count: 635
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 5	A	635	dengue virus type 3	Mutation(s): 0 EC: 2.7.7.48
UniProt
Find proteins for Q6YMS4 (Dengue virus type 3 (strain Sri Lanka/1266/2000)) Explore Q6YMS4 Go to UniProtKB: Q6YMS4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6YMS4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G Query on P6G Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	E [auth A], F [auth A], G [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.79 ?
R-Value Free: 0.209
R-Value Work: 0.177
R-Value Observed: 0.178
Space Group: C 2 2 2₁

Unit Cell:

Length ( ? )	Angle ( ? )
a = 161.32	α = 90
b = 177.61	β = 90
c = 57.82	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-02-27

Deposition Author(s):

Noble, C.G.

Lescar, J.

Revision History (Full details and data files)

Version 1.0: 2013-02-27
Type: Initial release
Version 1.1: 2013-07-31
Changes: Database references
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

4HHJ

Dengue serotype 3 RNA-dependent RNA polymerase

Conformational flexibility of the Dengue virus RNA-dependent RNA polymerase revealed by a complex with an inhibitor

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)